Once Lee saw the writing on the wall, so to speak, he may have felt it prudent to be the one setting an example. He knew if he didn't, his men would just come on back and join him. If he couldn't prove anything early on and after Lincoln was dead there wasn't much he could prove so he just went on with life. If he did know anything before leaving the US Army, he kept it to himself. It just doesn't seem in character for him to even try to speak ill or accuse Lincoln or any one else for that matter. Even if he saw or heard something that was just plain wrong in his mind, he'd have gone about righting it but not by pointing a finger. He was wise enough to understand that would be suicide.

Pam